Commit 8ebe012e authored by Haowen Zhang's avatar Haowen Zhang Committed by Li Song
Browse files

Separate single and paired end mapping metadata.

parent 267c10c2

src/chromap.h

+1 −0
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ 
#include "ksort.h"

#include "mapping_metadata.h"

#include "output_tools.h"

#include "paired_end_mapping_metadata.h"

#include "sequence_batch.h"

#include "temp_mapping.h"

src/mapping_metadata.h

+4 −83
Original line number Diff line number Diff line 
#ifndef MAPPINGMETADATA_H_

#define MAPPINGMETADATA_H_

#ifndef MAPPING_METADATA_H_

#define MAPPING_METADATA_H_



#include <algorithm>

#include <utility>
@@ -20,6 +20,7 @@ struct Candidate { 


class mm_cache;

class Index;

class PairedEndMappingMetadata;

template <typename MappingRecord>

class Chromap;
@@ -141,86 +142,6 @@ class MappingMetadata { 
  friend class Chromap;

};



class PairedEndMappingMetadata {

 public:

  inline void PreparedForMappingNextReadPair(int reserve_size) {

    mapping_metadata1_.PrepareForMappingNextRead(reserve_size);

    mapping_metadata2_.PrepareForMappingNextRead(reserve_size);



    F1R2_best_mappings_.clear();

    F2R1_best_mappings_.clear();

    F1F2_best_mappings_.clear();

    R1R2_best_mappings_.clear();



    F1R2_best_mappings_.reserve(reserve_size);

    F2R1_best_mappings_.reserve(reserve_size);

    F1F2_best_mappings_.reserve(reserve_size);

    R1R2_best_mappings_.reserve(reserve_size);

  }



  inline void MoveCandidiatesToBuffer() {

    mapping_metadata1_.MoveCandidiatesToBuffer();

    mapping_metadata2_.MoveCandidiatesToBuffer();

  }



  // Callback function to update all candidates.

  inline void UpdateCandidates(void (*Update)(std::vector<Candidate> &)) {

    mapping_metadata1_.UpdateCandidates(Update);

    mapping_metadata2_.UpdateCandidates(Update);

  }



  inline void SortMappingsByPositions() {

    mapping_metadata1_.SortMappingsByPositions();

    mapping_metadata2_.SortMappingsByPositions();

  }

  // inline void ClearAndReserveMinimizers(int reserve_size) {

  //  mapping_metadata1_.minimizers_.clear();

  //  mapping_metadata2_.minimizers_.clear();

  //  mapping_metadata1_.minimizers_.reserve(reserve_size);

  //  mapping_metadata2_.minimizers_.reserve(reserve_size);

  //}



  inline bool BothEndsHaveMinimizers() const {

    return !mapping_metadata1_.minimizers_.empty() &&

           !mapping_metadata2_.minimizers_.empty();

  }



  inline int GetMinSumErrors() const { return min_sum_errors_; }

  inline int GetSecondMinSumErrors() const { return second_min_sum_errors_; }

  inline int GetNumBestMappings() const { return num_best_mappings_; }

  inline int GetNumSecondBestMappings() const {

    return num_second_best_mappings_;

  }



  inline void SetMinSumErrors(int min_sum_errors) {

    min_sum_errors_ = min_sum_errors;

  }

  inline void SetSecondMinSumErrors(int second_min_sum_errors) {

    second_min_sum_errors_ = second_min_sum_errors;

  }

  inline void SetNumBestMappings(int num_best_mappings) {

    num_best_mappings_ = num_best_mappings;

  }

  inline void SetNumSecondBestMappings(int num_second_best_mappings) {

    num_second_best_mappings_ = num_second_best_mappings;

  }



 protected:

  MappingMetadata mapping_metadata1_;

  MappingMetadata mapping_metadata2_;



  int min_sum_errors_, second_min_sum_errors_;

  int num_best_mappings_, num_second_best_mappings_;



  std::vector<std::pair<uint32_t, uint32_t>> F1R2_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> F2R1_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> F1F2_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> R1R2_best_mappings_;



  template <typename MappingRecord>

  friend class Chromap;

};



}  // namespace chromap



#endif  // MAPPINGMETADATA_H_
 
#endif  // MAPPING_METADATA_H_

src/paired_end_mapping_metadata.h

0 → 100644
+94 −0
Original line number Diff line number Diff line 
#ifndef PAIRED_END_MAPPING_METADATA_H_

#define PAIRED_END_MAPPING_METADATA_H_



#include <algorithm>

#include <utility>

#include <vector>



#include "mapping_metadata.h"



namespace chromap {



class PairedEndMappingMetadata {

 public:

  inline void PreparedForMappingNextReadPair(int reserve_size) {

    mapping_metadata1_.PrepareForMappingNextRead(reserve_size);

    mapping_metadata2_.PrepareForMappingNextRead(reserve_size);



    F1R2_best_mappings_.clear();

    F2R1_best_mappings_.clear();

    F1F2_best_mappings_.clear();

    R1R2_best_mappings_.clear();



    F1R2_best_mappings_.reserve(reserve_size);

    F2R1_best_mappings_.reserve(reserve_size);

    F1F2_best_mappings_.reserve(reserve_size);

    R1R2_best_mappings_.reserve(reserve_size);

  }



  inline void MoveCandidiatesToBuffer() {

    mapping_metadata1_.MoveCandidiatesToBuffer();

    mapping_metadata2_.MoveCandidiatesToBuffer();

  }



  // Callback function to update all candidates.

  inline void UpdateCandidates(void (*Update)(std::vector<Candidate> &)) {

    mapping_metadata1_.UpdateCandidates(Update);

    mapping_metadata2_.UpdateCandidates(Update);

  }



  inline void SortMappingsByPositions() {

    mapping_metadata1_.SortMappingsByPositions();

    mapping_metadata2_.SortMappingsByPositions();

  }

  // inline void ClearAndReserveMinimizers(int reserve_size) {

  //  mapping_metadata1_.minimizers_.clear();

  //  mapping_metadata2_.minimizers_.clear();

  //  mapping_metadata1_.minimizers_.reserve(reserve_size);

  //  mapping_metadata2_.minimizers_.reserve(reserve_size);

  //}



  inline bool BothEndsHaveMinimizers() const {

    return !mapping_metadata1_.minimizers_.empty() &&

           !mapping_metadata2_.minimizers_.empty();

  }



  inline int GetMinSumErrors() const { return min_sum_errors_; }

  inline int GetSecondMinSumErrors() const { return second_min_sum_errors_; }

  inline int GetNumBestMappings() const { return num_best_mappings_; }

  inline int GetNumSecondBestMappings() const {

    return num_second_best_mappings_;

  }



  inline void SetMinSumErrors(int min_sum_errors) {

    min_sum_errors_ = min_sum_errors;

  }

  inline void SetSecondMinSumErrors(int second_min_sum_errors) {

    second_min_sum_errors_ = second_min_sum_errors;

  }

  inline void SetNumBestMappings(int num_best_mappings) {

    num_best_mappings_ = num_best_mappings;

  }

  inline void SetNumSecondBestMappings(int num_second_best_mappings) {

    num_second_best_mappings_ = num_second_best_mappings;

  }



 protected:

  MappingMetadata mapping_metadata1_;

  MappingMetadata mapping_metadata2_;



  int min_sum_errors_, second_min_sum_errors_;

  int num_best_mappings_, num_second_best_mappings_;



  std::vector<std::pair<uint32_t, uint32_t>> F1R2_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> F2R1_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> F1F2_best_mappings_;

  std::vector<std::pair<uint32_t, uint32_t>> R1R2_best_mappings_;



  template <typename MappingRecord>

  friend class Chromap;

};



}  // namespace chromap



#endif  // PAIRED_END_MAPPING_METADATA_H_

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